This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Abstract

Starvation is a complex adaptive response to insufficiency of nutrients that has been known to implicate a number of stress networks, and modulate pathogenicity and antibiotic resistance in bacteria. However, naturally occurring abrupt elimination of nutrients and prolonged periods of their complete absence, e.g. when bacteria are placed in natural or artificial water reservoirs, are qualitatively different from in-culture late stationary phase energy source diminution. Despite the obvious importance of proteomic investigation of bacteria exposed to nutrient deficiency, no comprehensive study on the subject has been published. In order to address the said shortage of knowledge, we decided to quantitatively look into the proteome-level alterations elicited by the complete lack of nutrients that constitute a viable source of carbon, i.e. carbon starvation, in the Escherichia coli HT115-derived SLE1 strain cells using the combination of label-free and SILAC-based proteomics. As a result, we obtained protein ratios for 1,757 and 1,241 protein groups for each technique respectively, 2D-annotated the quantifiable proteins present in both datasets, identified over- and underrepresented Gene Ontology terms, and isolated protein groups ≥2-fold up- and downregulated in response to carbon starvation (44 and 36 protein groups respectively). We observed upregulation of proteins implicated in various stress-related networks, most notably those that constitute the Gene Ontology term 'Biological adhesion', as well as various terms related to stress. Additionally, we identified several uncharacterized proteins, and our report is the first to ascribe them to a stress-induced proteome. Our data are available via ProteomeXchange with identifier PXD003255 and DOI:10.6019/PXD003255.

Over- and underrepresented pathways (David)

Additional Information

Competing Interests

Author Contributions

Rakhan Aimbetov conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Vasily Ogryzko conceived and designed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

ProteomeXchange/PRIDE

http://www.ebi.ac.uk/pride/archive/projects/PXD003255

Project Name: The effect of carbon starvation on the Escherichia coli SLE1 proteome.

Project accession: PXD003255

Project DOI: 10.6019/PXD003255

Funding

This work was supported by Association pour la Recherche sur le Cancer (subvention no. SFI20121205936 to VO, and PDF20130606592 to VO
and RA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Follow this preprint for updates

"Following" is like subscribing to any updates related to a preprint.
These updates will appear in your home dashboard each time you visit PeerJ.

You can also choose to receive updates via daily or weekly email digests.
If you are following multiple preprints then we will send you
no more than one email per day or week based on your preferences.

Note: You are now also subscribed to the subject areas of this preprint
and will receive updates in the daily or weekly email digests if turned on.
You can add specific subject areas through your profile settings.